3U54

Crystal structure (Type-1) of SAICAR synthetase from Pyrococcus horikoshii OT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: insights into thermal stability

Manjunath, K.Kanaujia, S.P.Kanagaraj, S.Jeyakanthan, J.Sekar, K.

(2013) Int.J.Biol.Macromol. 53: 7-19

  • DOI: 10.1016/j.ijbiomac.2012.10.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first native crystal structure of Phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) from a hyperthermophilic organism Pyrococcus horikoshii OT3 was determined in two space groups H3 (Type-1: Resolution 2.35Å) and in C ...

    The first native crystal structure of Phosphoribosylaminoimidazole-succinocarboxamide synthetase (SAICAR synthetase) from a hyperthermophilic organism Pyrococcus horikoshii OT3 was determined in two space groups H3 (Type-1: Resolution 2.35Å) and in C222(1) (Type-2: Resolution 1.9Å). Both are dimeric but Type-1 structure exhibited hexameric arrangement due to the presence of cadmium ions. A comparison has been made on the sequence and structures of all SAICAR synthetases to better understand the differences between mesophilic, thermophilic and hyperthermophilic SAICAR synthetases. These SAICAR synthetases are reasonably similar in sequence and three-dimensional structure; however, differences were visible only in the subtler details of percentage composition of the sequences, salt bridge interactions and non-polar contact areas.


    Organizational Affiliation

    Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosylaminoimidazole-succinocarboxamide synthase
A, B
238Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: purC
EC: 6.3.2.6
Find proteins for O57978 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O57978
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BU1
Query on BU1

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Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 95.420α = 90.00
b = 95.420β = 90.00
c = 148.631γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MAR345dtbdata collection
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references